3-16366950-C-T

Variant names:

• chr3-16366950-C-T
• rs9835911
• NM_015150.2:c.1030+3126G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015150.2(RFTN1):​c.1030+3126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,378 control chromosomes in the GnomAD database, including 13,217 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (13217 hom., cov: 32)
• Consequence: RFTN1 NM_015150.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 3 publications found

Genes affected

RFTN1 (HGNC:30278): (raftlin, lipid raft linker 1) Enables double-stranded RNA binding activity. Involved in B cell receptor signaling pathway; membrane raft assembly; and positive regulation of growth rate. Acts upstream of or within dsRNA transport; response to exogenous dsRNA; and toll-like receptor 3 signaling pathway. Located in endosome; membrane raft; and plasma membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000287377 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RFTN1	NM_015150.2	c.1030+3126G>A		intron_variant	Intron 6 of 9	ENST00000334133.9	NP_055965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RFTN1	ENST00000334133.9	c.1030+3126G>A		intron_variant	Intron 6 of 9	1	NM_015150.2	ENSP00000334153.4
RFTN1	ENST00000432519.5	c.922+3126G>A		intron_variant	Intron 5 of 8	1		ENSP00000403926.1
RFTN1	ENST00000483671.1	n.309+3126G>A		intron_variant	Intron 2 of 5	2
ENSG00000287377	ENST00000653928.1	n.348-2729C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61348 AN: 151260 Hom.: 13194 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.362

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.406 AC: 61428 AN: 151378 Hom.: 13217 Cov.: 32 AF XY: 0.378 AC XY: 27859 AN XY: 73716

African (AFR) AF: 0.668 AC: 27400 AN: 41010

American (AMR) AF: 0.401 AC: 6111 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1473 AN: 3452

East Asian (EAS) AF: 0.203 AC: 1050 AN: 5168

South Asian (SAS) AF: 0.318 AC: 1515 AN: 4768

European-Finnish (FIN) AF: 0.288 AC: 3037 AN: 10542

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.290 AC: 19683 AN: 67904

Other (OTH) AF: 0.361 AC: 758 AN: 2102

Alfa AF: 0.343 Hom.: 12419

Asia WGS AF: 0.290 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.62
DANN	Benign	0.69
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9835911; hg19: chr3-16408457;